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Are Your Supplements Turning into Deadly Pathogens in the Gut?

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“The human body houses somewhere in the neighborhood of one hundred trillion bacteria within the body—about 3.5 pounds worth.” But don’t think of that fact as a new method for losing weight – rather make sure you turn the porch light on and lay out the guest towels: those bacteria, including 400-500 different species in the gut alone, are responsible for your health as much as or more than the food we eat.

In fact, the bacteria in your body outnumber your own cells ten to one. It’s a good thing they’re friendly, isn’t it?

With that ratio, if the bacteria wanted to take over, they certainly would have the means.

Many people, most notably Jordan Rubin of The Maker’s Diet and Garden of Life supplements, credit soil-based organisms (SBOs) for their miraculous recovery. In Rubin’s case, after seeing over 60 specialists all around the world for his severe Crohn’s Disease and related complications, it was SBOs that finally brought him back literally from the brink of death.

Why the controversy?

Soil-based organisms reproduce differently than other bacteria that are normally part of our flora in that they are spore-forming. Because of these spores, if a person does not have enough of their own healthy gut flora to compete with the SBOs, it opens the door for them to become pathogenic.

You read that right.

Supplements you take on purpose to improve your health and your gut flora could actually turn against you and become pathogens (harmful bacteria) themselves.

What We Don’t Know About Probiotics

The trouble with finding good information about probiotics is that research is sorely lacking. For the last century or so, our researchers and doctors have been focused on fighting the enemy rather than learning about the weapons we can utilize to protect ourselves. Most of the studies we have access to teach us what disease does to the human body and then test the effectiveness of man-made weapons, like antibiotics, in fighting them.

It’s been a very recent shift that we’re even looking into our own flora, the millions and trillions of beneficial bacteria that our bodies already possess, and how that can be a line of defense against disease. Because of that, we don’t really know how probiotics work or even how our own gut flora operates with very much detail.

There are a few studies referenced here at the Wikipedia page on microbiomes, but it’s clear that we have a lot to learn.

Currently, Washington University is host to the government-funded Human Microbiome Project, which seeks to “characterize the microbial communities found at several different sites on the human body, including nasal passages, oral cavities, skin, gastrointestinal tract, and urogenital tract, and to analyze the role of these microbes in human health and disease.” (source)

They’re embarking on fascinating and vitally important work, and countries all over the world are also sparking an interest in the bacteria we carry around. Here’s an interesting and exciting Q&A with the Associate Director of the Genome Institute if you’d like to learn more.

One of the only studies so far involved a mere 100 people, all from the same geographic area, and although it is helpful, it’s simply too narrow to extrapolate data to the entire population quite yet. Because everybody’s resident bacteria and pathogens are different, we can pretty much say that we don’t really understand our own internal probiotics yet, and we know even less about what probiotic supplements do in the body.

No studies have been done to determine if probiotic supplementation could ever repopulate one’s gut permanently, changing the resident bacteria to a properly balanced flora. In fact, some research does show that within two weeks, most supplemented probiotics exit the gut and are excreted.

Since our resident friendly bacteria make up 70% of our immune system, responsible for fighting viral, bacterial, and fungal infections, it’s exciting that researchers are finally looking into the little guys.

Where Does Our Gut Flora Come From?

Why all this talk about unhealthy, unbalanced flora? It’s widely believed that, at birth, babies’ guts are sterile of all bacteria. Beginning at birth and continuing through the first two years of life, the tiny human being becomes residence for various bacteria, beneficial or detrimental depending on the environment provided in the gut and what the baby comes into contact with.

Think it’s a good idea to let baby have sugar before age two? My first two babies didn’t have desserts until after age one, but poor John…there’s no way I’m letting him have sweets, if I can possibly stop it, until age two now that I’ve read that fact! Sugars and refined flours are food for pathogens, dangerous bacteria. If you feed them, they will come.

My oldest son, now seven, clearly has bacterial issues and has needed antibiotics numerous times. He had antibiotics at birth, had sugar and flour in things like Cheerios well before age one, and has certainly had his fair share of white flour in his lifetime. Le sigh. I doubt it’s a coincidence, and I think I’ll try to sneak probiotics capsules into his smoothie more often.

Do You Eat Dirt?

The probiotic strains in yogurt and kefir are usually lactobacilli or bifidobacteria (I wonder if I’m making those plural correctly…), both of which are part of our resident bacteria, generally. The probiotics in the Garden of Life supplements are “soil-based organisms,” which are bacteria that literally live in the soil. They are still friendly to humans, but they’re not automatically part of our resident flora. “Transient micro organisms [like SBOs] are different from resident micro organisms in that they do not take up permanent residence in the gastrointestinal tract. Instead, they establish small colonies for brief periods of time before dying off or being flushed from the intestinal system via normal digestive processes, or by peristaltic bowel action.” source

Until about 100 years ago, SBOs were a regular part of people’s diets. When food processing got between farmers and eaters, the food chain, in a sense, was literally interrupted, and consumption of SBOs drastically diminished. Also I must imagine that the clean-to-the-point-of-sterile society we live in has reduced our interaction with these friendly little guys, further removing SBOs from our guts.

I’ve always wondered aloud while watching my babies put everything in their mouths how that could possibly be a good evolutionary trait. Maybe the good Lord made a little “oops” on that one, since dirty things and items small enough to choke a baby don’t seem helpful when placed into the mouth at mind-warping speed by chubby little fingers.

Now, I understand.

Human babies were created to crawl around in the dirt, getting intimate with the soil-based organisms they might find. Putting everything in the world in their mouths is a unique form of inoculation, brilliant in its simplicity. Those babies under two are working to populate their guts with healthy bacteria, and who knew? Eating dirt is a darn good idea.

In fact, research shows that children do better than adults with SBO supplements. The theory is that their little bodies are primed for the SBOs, and that perhaps, adults who simply haven’t been exposed to them much in the past can’t quite handle the influx of SBOs when they start a supplementation regimen. Here’s where the story gets ugly…

Too Much Good Gut Bacteria?

Because so many adults have damaged flora, they don’t have enough of their own healthy bacteria to even stake a claim in their gut. Soil-based organisms, being spore-forming, proliferate very rapidly, and one theory is that without enough resident bacteria to hold up the front lines, the SBOs literally take over a person’s gut, becoming pathogenic in their aggression.

“Research from California has concluded that a deficiency of medicinal ‘superbugs’ – known as Soil Based Organisms (SBO) – from our soil and food chain may be responsible”(1) for intestinal illnesses and diseases such as irritable bowel syndrome (IBS), Crohn’s disease, colitis, candidiasis, and colon cancer. source

Because we’re deficient, some people can’t handle them when they come. Dr. Doran-Fisher has anecdotal evidence of clients who took a turn for the worse when they started SBO supplements and improved once they used a refrigerated strain with lactobacilli and bifidobacteria.

If you’re taking a probiotic and it’s not doing anything good for you, and especially if you noticed negative changes after an initial possible issue with constipation or flatulence as the body adjusts the the new bacterial balance, stop and look for a new one.

This pathogenic SBO issue really is a problem, and I’m hopeful that some of the newer research coming out will determine if adults who haven’t been exposed to SBOs can somehow rebalance their gut first and then use SBOs. Check this out:

Studies conducted in regard to SBOs provide evidence that “without SBO’s to police digestion our bowels often end up as toxic waste dumps for rotting faecal matter which builds layer upon layer until the intestinal wall cannot absorb anything useful and we start to drown on our own toxins….With an intestinal wall starved of nutrients however it can quickly become porous like Swiss Cheese leading to the much maligned ‘Leaky Gut Syndrome’ where undigested waste food can leak into the blood leading to fierce immune reactions ”(5) By supplementing SBOs into daily dietary habits, the occurrences illnesses and diseases such as these may be reduced or altogether prevented. source

In other words, because we’re deficient in soil-based organisms in our clean society, we’re getting sick. Because we’re sick and out of balance, some of us might not be able to handle getting the SBOs that could help us, and they’ll make us sicker instead.

UPDATE 7/10/12: I found a few more sources about soil-based organisms being harmful. This one is particularly packed with academic sources at the end, AND it discusses how Garden of Life has changed their formula to remove all but one SBO. This one touches on nomenclature in the probiotic world.

If You Poop Once a Day, You’re Not “Regular”

My 4-year-old will tell you that “brown, orange, red, brown, orange, red” is a pattern…but that doesn’t mean it will look good on your shirt.

Just because your bowels follow a regular pattern doesn’t mean you have healthy digestion.

Healthy digestion is determined by the consistency of your stool (see here for a lovely pictorial chart), frequency of elimination (2 or more times per day, every time you eat usually optimal), and how satisfied you feel when you’re finished. Click here for some questions to help you consider your own digestion.

I always thought once a day was great, and as long as I wasn’t in pain, I wasn’t constipated.

Wrong.

When I give up all grains and sugar (for Lent), something changes. I end up moving my bowels just about every time I sit down to urinate. Thank you for not grimacing or laughing as you read that.

When the grains and sugar come back, things immediately change. This is something I had never realized in 30 years of living, people! You really can learn new things about your body, even when you think you’re in perfect health.

Some odd issues have come up in my personal health lately – I’ll share more once I feel like I’ve beaten them – but one result of my battle against pathogens in my body was to switch up my probiotic regimen. I stopped taking Garden of Life probiotics and started eating my homemade lacto-fermented sauerkraut and kimchi (which I learned to make via the fermented foods eCourse) at every meal, and I ate a probiotic chocolate bar every day for two weeks.

I always thought people were a little (or a lot) off their rockers when we’d talk sauerkraut, which I’ve always despised despite the half-Polish blood coursing through my veins, and they would tell me that I would begin to crave the stuff after eating it for a while.

No way.

The only thing sauerkraut will make me do is cringe, I always thought.

During the time of really working on my flora imbalance, intellectually I knew I needed it at every meal, so I forced myself.

And I couldn’t believe it, but after just a few days of regular fermented foods consumption, I did start to want a bite when I opened the refrigerator door for a snack. I’m working on enjoying it (and remembering it) even more.

Do You Take Probiotics?

UPDATE 2015: For a few years, we’ve actually been taking the Miessence probiotics, both powder and liquid, and we’re very happy with them. It seems that they help me beat back some nasty candida, for starters. And the liquid is super super easy to give to kids, a welcome relief!

I also want you to read this post with a perspective from another naturopath on the refrigerated issue (myth?).

I never thought I had poor digestion, and I always thought of myself as the picture of health. But maybe I didn’t eat enough dirt as a child. I’m guessing, not as a medical professional of any kind, but as a thinking person in the 20th century, that all Americans should probably take a probiotic supplement.

And if you don’t see a change in two weeks, you should probably try something different. Look for probiotics in the refrigerated section of your health food store. If it’s not refrigerated, it’s either SBO probiotics or something is amiss (UPDATE 2018: I don’t think that’s true anymore! More research needed…).

Some Quality Probiotics

Some of these I’ve used, some I’m planning to use, and some have been recommended by friends and professionals alike. It’s good to remember a few things about probiotics: 1. People should get different colonies of probiotics, so switching brands/strains every so often (6 weeks?) is good practice. 2. What works great for one person’s needs doesn’t always work for another. These can be very different! A one-day trial to Probiotic Advisor might help you get up on current research quickly if you’re really digging in; otherwise, here are some to narrow down the thousands of brands out there:

Just Thrive Probiotics – this one can be taken during antibiotics and not be rendered ineffective, which almost all other probiotics are! It’s the top recommended probiotic overall by Paleo Mom Sarah Ballantyne. 😮 (Be sure to use the code Katie15 for 15% off; also found on Amazon and from Perfect Supplements where you can use the coupon KS10 for 10% off!)

RightBioticsRX – the top recommended probiotic of all soil-based options by an expert I’ve been working with. Read more here. Use Subscribe and Save to save more!

Note: If you’re struggling with digestion, especially constipation, or you feel like you really need to populate your gut with healthy probiotics, I would recommend Saccharomyces Boulardii in addition to any other you choose (except the 2 above which include this strain). Saccharomyces Boulardii is research-proven to get through the digestive tract without being killed, which is rare.

Balance One probiotics with a unique time-release formula (watch for discounts on the site; there’s almost always one there!)

Miessence Liquid Probiotic – notes: this is the easiest for kids to take because it’s liquid on a spoon, no powder to hide in smoothies and no capsules to swallow. If you’re on a no-sweetener diet of any kind, it does have agave so could be a no-no. Gluten-free.

Miessence Powder Probiotic – notes: must be hidden in a smoothie but is less expensive than the above. Not gluten-free. Helped me beat a candida rash when nothing else could.

About Katie Kimball @ Kitchen Stewardship

Katie Kimball is a trusted educator and author of 8 real food cookbooks. She is passionate about researching natural remedies and making healthy cooking easier for busy families. She’s been featured on media outlets like ABC, NBC and First for Women magazine as well as contributing regularly on the FOX Network. Over the last 10 years, Katie has spoken prolifically at conferences, online summits and podcasts and become a trusted authority and advocate for children’s health. Busy moms look to this certified educator for honest, in-depth natural product reviews and thorough research. She often partners with health experts and medical practitioners to deliver the most current information to the Kitchen Stewardship community. In 2016 she created the #1 bestselling online kids cooking course, Kids Cook Real Food, helping thousands of families around the world learn to cook. A mom of 4 kids from Michigan, she is a Stress Mastery Educator and member of the American Institute of Stress.

117 Bites of Conversation So Far

Bacillus HU36®, being a spore, offers advantages of better colonization and survival through the digestive track when compared to non-spore probiotic organisms; it also offers claims related to the most bioavailable form of antioxidants and carotenoids.

More details:
https://www.synergialifesciences.com/bacillus-indicus-strain-spore-probiotic-HU36.html

Great article! I am thinking of starting Garden of Life because of the number of strains, but also because of the strain of SBO in it. I have had horrible Heartburn my whole life and I am trying to wean myself off of PPIs. I understand the risks, but I am pretty healthy. Have you heard anymore on the research for this Bacillus subtillis? Also, I wanted to correct you on 1 statement. You wrote “had sugar and flour in things like Cheerios well before age one”, but Cheerios has never had flour and has always been oat based. However, they have made efforts now to remove any stray wheat, rye, and barley grains to guarantee it is Gluten-Free.

I let my children play naked in our (organic) garden every year to help them grow their intestinal flora, so I loved to read that section about eating dirt. ^.^

I do have to say, though I haven’t taken this probiotic myself, there actually have been successful studies done on the SBO probiotic, Prescript-Assist. It appears to get high marks actually. As with all supplements, there are people who feel great taking it, and there are people who don’t. Also I know that BioKult has at least one SBO in it as well. That one was developed by Dr. Campbell McBride. I am a holistic nutritional consultant, and I can say she is a source I trust. I think the bottom line is, we are all different, so what will work for one may not work for another. What will work for one may be pathogenic for another. Anything out of balance *can* be pathogenic. Anything. People from different parts of the planet will have different “normal flora”, so while SBO’s may not work for everyone, they do work for some. And really that is a good thing for those people. Cheers.

What about diatomaceous earth? Is that a soil based/spore forming organism? I’ve taken it before as a supplement with no adverse reactions. However recently I took it two days in a row and I’ve had upset stomach with diarrhea ever since (4 days now). My diet has not been the greatest lately and I haven’t been using probiotics or fermented veggies in awhile. So my two questions are: 1. Can diatomaceous earth also cause these pathogens. 2. How do you kill them and restore good health?

Diatomaceous Earth is microscopic shells of fossilized creatures. It is not alive itself. Many people take it to help them get rid of parasites. There has been a concern over the amounts of heavy metals it contains, and that it can cause severe lung problems if inhaled. Proponents of DE say that it is electrically charged in such a way that it will pull heavy metals to it, and thus carry them out of the body. So even though it may contain heavy metals, it is said to clear them out as well. It is one of those areas where people need to research and decide whether they want to take the risks to receive the benefits. There are many success stories from having taken it, though.

I am here after trying a small amount of SBO probiotics last night. Everyone seems to be recommending them right now so I thought I’d give them a whirl. Well, I don’t feel too good at all! I slept very badly last night and felt very tense and anxious and my belly feels bloated. I took the SBOs as they are supposed to be better for those with histamine intolerance, which I have.

Back to the drawing board for me…I’m thinking of just giving up on probiotics at this point until they are better understood.

Phil,
I just wrote a related post a few hours ago that you might want to read! Don’t give up on probiotics; they’re one of the few things we DO understand about the microbiome in general, that they’re good for you. http://www.kitchenstewardship.com/2014/07/31/the-care-and-feeding-of-your-microbiome/

Your yucky feeling could potentially be die-off (the good probiotics are nudging out or killing the bad bugs in there) and would go away after a while, or you might just prefer other strains of probiotics.

You didn’t give evidence other than the naturopath’s anecdotal advice. By that token, let’s include links to the many many anecdotal stories of people improving with SBOs (stories not sponsored by a soy-containing corporate produce clearly standing to gain by people fleeing from SBOs).

The SBO fear story has been largely debunked and thought to be drummed up by the other non-SBO hawking probiotic makers.

You can read the excellent and trust-worthy Chris Kresser here on the proven non-pathenogenic Prescript Assist. He treats his patients with PA with great success. One anecdote plus science v fearmongering.

I’ve heard great things about Fermented foods, so I went out and bouht raw, 100% organic Kimchi: bad mistake.

All it took was a teaspoon to give me some sharp stomach pains. And I eat healthy — lots of cruciferous vegetables and fruits. I will say, though, that Sauerkraut (unsalted and organic) does fall well with me.

As far as Probiotic supplements… meh. The only one I’d recommend is Bio-K, they’re these small shots that you take, they have around 5 billion cultures. It’s not worth taking the risk of using a supplement based off of someone who thinks we’re better off because we just don’t consume anymore cultured-foods.

Kimchi is Asian. Bulgarian Kefir (which is found in the Garden of Life probiotics is a Bulgarian culture-thing).

I’m following my ancestral diet, mostly Mediterranean, that’s where I thrive the most. Enough of these ‘fads’, they’re only causing more harm than good.

I would take with a grain of salt the idea that a person must poop 2-3 times a day to be healthy. That belief was started and promoted by some rather neurotic individuals such as John Harvey Kellogg, who recommended daily enemas. They were obsessed with colons and poop and weird extreme diets etc. Traditional Chinese medicine considers a daily bowel movement to be ideal, 2 to be ok and more than that to be a sign of imbalance that needs treated. Babies poop so much because of the extreme digestibilty of breast milk that passes quickly through their tracts. Mine still didn’t poop more than a couple or three times a day though. Once they were on food and off breast milk though it reduced to 1-2 times a day. Many things will influence the times per day such as how low or high residue the diet, whether or not you are consuming things that have laxative properties, your rate of metabolism, etc. I personally feel best with one to 2 movements a day. One is fine generally. I have heard the argument that if one eats 3 times a day one should poop 3 times but logically this just doesn’t hold up. Most of what you eat gets digested and absorbed so what goes in will not equal what comes out. Most of what comes out is bacteria. Estimates I’ve seen are anywhere from 60 to 90 percent.

Just thought I would help you to think about where the info you accept might have come from and think a little more critically so as not to latch onto things that could end up causing you to think you have a health problem you might not have and trying to treat an imaginary problem thereby causing yourself mental emotional and physical distress and maybe even harm for nothing. It is important to get info from numerous sources use common sense.

This is what a FB friend said:
‘It doesn’t seem to make a whole lot of sense since soil organisms work to change the ph level of the colon to a more acidic environment which enables the growth of healthy bacteria and discourages the growth of pathogens since pathogens can only thrive in an alkaline environment.’

I was wondering if you have heard of the prescript assist probiotics? If not do you think you could look at the link and tell me what you think? http://www.prescript-assist.com/products/
I would appreciate it. I have been debating between two brands, the prescript assist, but now I’m not sure because of this article, and the other is klaire labs Ther-biotic complete. Thank you in advance!

Please remember that I’m just a gal who reads a lot and spends way too much time in her kitchen. I’m not a doctor, nurse, scientist, or even a real chef, and certainly the FDA hasn't evaluated anything on this blog. Any products mentioned are not intended to diagnose, treat, cure, or prevent any disease. Please talk to your health professional (or at least your spouse) before doing anything you might think is questionable. Trust your own judgment…I can’t be liable for problems that occur from bad decisions you make based on content found here.

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